Framework-R-D · Copilot · Nov 16, 2025 · Mar 4, 2026 · Mar 4, 2026 · Mar 9, 2026
diff --git a/.gitignore b/.gitignore
@@ -46,6 +46,10 @@ __pycache__/
 *.pyc
 *.pyo
 
+# Documentation build output
+docs/doxygen/
+docs/build/
+
 # macOS
 .DS_Store
 # act (local workflow testing)

diff --git a/docs/Doxyfile b/docs/Doxyfile
@@ -0,0 +1,29 @@
+# Doxyfile
+
+# -- Project settings --------------------------------------------------------
+PROJECT_NAME      = "Phlex"
+PROJECT_BRIEF     = "A framework for parallel, hierarchical, and layered execution of data-processing algorithms"
+QUIET             = YES
+
+# -- Input and output directories --------------------------------------------
+# Paths are relative to the repository root; invoke as: doxygen docs/Doxyfile
+INPUT             = phlex form
+OUTPUT_DIRECTORY  = docs/doxygen
+RECURSIVE         = YES
+
+# -- Output formats ----------------------------------------------------------
+GENERATE_HTML     = NO
+GENERATE_LATEX    = NO
+GENERATE_XML      = YES
+XML_OUTPUT        = xml
+
+# -- Source code parsing -----------------------------------------------------
+EXTRACT_ALL       = YES
+WARN_IF_UNDOCUMENTED = NO
+ENABLE_PREPROCESSING = YES
+MACRO_EXPANSION  = YES
+FILE_PATTERNS     = *.hpp *.cpp
+EXCLUDE_PATTERNS  = */detail/*
+# Help Doxygen with some of the more complex macros
+PREDEFINED        = "BOOST_DLL_ALIAS(a,b)=" \
+                    "PHLEX_DETAIL_REGISTER_PLUGIN(...)="
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1,3 @@
+sphinx>=9.1,<10
+breathe>=4.36,<5
+sphinx-rtd-theme>=3.1,<4
diff --git a/docs/source/api/concurrency.rst b/docs/source/api/concurrency.rst
@@ -0,0 +1,6 @@
+concurrency
+============
+
+.. doxygenstruct:: phlex::concurrency
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/configuration.rst b/docs/source/api/configuration.rst
@@ -0,0 +1,6 @@
+configuration
+==============
+
+.. doxygenclass:: phlex::configuration
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/declared_fold.rst b/docs/source/api/declared_fold.rst
@@ -0,0 +1,6 @@
+declared_fold
+==============
+
+.. doxygenclass:: phlex::experimental::declared_fold
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/declared_transform.rst b/docs/source/api/declared_transform.rst
@@ -0,0 +1,6 @@
+declared_transform
+===================
+
+.. doxygenclass:: phlex::experimental::declared_transform
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/declared_unfold.rst b/docs/source/api/declared_unfold.rst
@@ -0,0 +1,6 @@
+declared_unfold
+================
+
+.. doxygenclass:: phlex::experimental::declared_unfold
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/framework_graph.rst b/docs/source/api/framework_graph.rst
@@ -0,0 +1,6 @@
+framework_graph
+================
+
+.. doxygenclass:: phlex::experimental::framework_graph
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/graph_proxy.rst b/docs/source/api/graph_proxy.rst
@@ -0,0 +1,6 @@
+graph_proxy
+=============
+
+.. doxygenclass:: phlex::experimental::graph_proxy
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/handle.rst b/docs/source/api/handle.rst
@@ -0,0 +1,6 @@
+handle
+=======
+
+.. doxygenclass:: phlex::handle
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/module_graph_proxy.rst b/docs/source/api/module_graph_proxy.rst
@@ -0,0 +1,6 @@
+module_graph_proxy
+===================
+
+.. doxygenclass:: phlex::experimental::module_graph_proxy
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/product_store.rst b/docs/source/api/product_store.rst
@@ -0,0 +1,6 @@
+product_store
+==============
+
+.. doxygenclass:: phlex::experimental::product_store
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/products.rst b/docs/source/api/products.rst
@@ -0,0 +1,6 @@
+products
+=========
+
+.. doxygenclass:: phlex::experimental::products
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/registrar.rst b/docs/source/api/registrar.rst
@@ -0,0 +1,6 @@
+registrar
+==========
+
+.. doxygenclass:: phlex::experimental::registrar
+   :members:
+   :undoc-members:
diff --git a/docs/source/api/source_graph_proxy.rst b/docs/source/api/source_graph_proxy.rst
@@ -0,0 +1,6 @@
+source_graph_proxy
+===================
+
+.. doxygenclass:: phlex::experimental::source_graph_proxy
+   :members:
+   :undoc-members:
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -0,0 +1,29 @@
+# mypy: ignore-errors
+"""Sphinx configuration for Phlex documentation."""
+
+# -- Project information -----------------------------------------------------
+
+project = "Phlex"
+copyright = "2025-2026, The Phlex Developers"
+author = "The Phlex Developers"
+release = "0.1.0"
+
+# -- General configuration ---------------------------------------------------
+
+extensions = [
+    "breathe",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+# -- Options for HTML output -------------------------------------------------
+
+html_theme = "sphinx_rtd_theme"
+
+# -- Breathe configuration -------------------------------------------------
+
+breathe_projects = {
+    "Phlex": "../doxygen/xml/",
+}
+breathe_default_project = "Phlex"
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -0,0 +1,35 @@
+.. Phlex documentation master file, created by
+   sphinx-quickstart on Tue Nov 15 14:29:55 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Phlex's documentation!
+==================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Plugin entry points:
+
+   api/module_graph_proxy
+   api/source_graph_proxy
+   api/graph_proxy
+   api/framework_graph
+   api/registrar
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Algorithm nodes:
+
+   api/declared_transform
+   api/declared_fold
+   api/declared_unfold
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Data model:
+
+   api/configuration
+   api/handle
+   api/concurrency
+   api/product_store
+   api/products